Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008033.1 Hibiscus syriacus cultivar Beakdansim tig00110515_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3048429
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 14
Found at i:2990616 original size:45 final size:45
Alignment explanation
Indices: 2990533--2990618 Score: 109
Period size: 45 Copynumber: 1.9 Consensus size: 45
2990523 AAGACACGTT
* * * **
2990533 CTTTGAATGAAAAATGGTGTCCTTTTGCTGTTTGATGGATAAGTC
1 CTTTGAATGAAAAATGATGGCCTTTTGCTGCTCAATGGATAAGTC
* *
2990578 CTTTGAATGAAAAATTATGGCCTTTTGTTGCTCAATGGATA
1 CTTTGAATGAAAAATGATGGCCTTTTGCTGCTCAATGGATA
2990619 TTTCTTTTGG
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
45 34 1.00
ACGTcount: A:0.27, C:0.12, G:0.22, T:0.40
Consensus pattern (45 bp):
CTTTGAATGAAAAATGATGGCCTTTTGCTGCTCAATGGATAAGTC
Found at i:2992809 original size:16 final size:16
Alignment explanation
Indices: 2992779--2992828 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
2992769 AAGTAATGAA
2992779 AATAAGAAAAGATGAAAG
1 AATAAG-AAA-ATGAAAG
*
2992797 AATAAGAAAATGAAAT
1 AATAAGAAAATGAAAG
*
2992813 AGTAAGAAAAT-AAAG
1 AATAAGAAAATGAAAG
2992828 A
1 A
2992829 TAACTTACAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
15 4 0.14
16 16 0.55
17 3 0.10
18 6 0.21
ACGTcount: A:0.68, C:0.00, G:0.18, T:0.14
Consensus pattern (16 bp):
AATAAGAAAATGAAAG
Found at i:2993038 original size:6 final size:6
Alignment explanation
Indices: 2993027--2993070 Score: 54
Period size: 6 Copynumber: 7.2 Consensus size: 6
2993017 GATGTTGGAG
*
2993027 TCTTTT TC-TTT TCTTTT TGTTTT TCTTCTT TCTTTT TCTCTTT T
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTT-TT TCTTTT TCT-TTT T
2993071 TGTTGCAGTA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
5 5 0.15
6 18 0.55
7 10 0.30
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (6 bp):
TCTTTT
Found at i:2993050 original size:12 final size:12
Alignment explanation
Indices: 2993027--2993070 Score: 54
Period size: 13 Copynumber: 3.6 Consensus size: 12
2993017 GATGTTGGAG
2993027 TCTTTTTC-TTT
1 TCTTTTTCTTTT
*
2993038 TCTTTTTGTTTT
1 TCTTTTTCTTTT
2993050 TCTTCTTTCTTTT
1 TCTT-TTTCTTTT
2993063 TCTCTTTT
1 TCT-TTTT
2993071 TGTTGCAGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 7 0.25
12 7 0.25
13 13 0.46
14 1 0.04
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (12 bp):
TCTTTTTCTTTT
Found at i:2993308 original size:15 final size:15
Alignment explanation
Indices: 2993290--2993360 Score: 54
Period size: 15 Copynumber: 5.4 Consensus size: 15
2993280 AAGAAGAAAG
2993290 GAAATGATAAGAATT
1 GAAATGATAAGAATT
*
2993305 GAAATG----G-ATA
1 GAAATGATAAGAATT
2993315 GAAATGATAAGAATT
1 GAAATGATAAGAATT
*
2993330 GAAATG----G-ATA
1 GAAATGATAAGAATT
2993340 GAAATGATAAGAATT
1 GAAATGATAAGAATT
2993355 GAAATG
1 GAAATG
2993361 GATAGAAATG
Statistics
Matches: 42, Mismatches: 4, Indels: 20
0.64 0.06 0.30
Matches are distributed among these distances:
10 16 0.38
11 2 0.05
14 2 0.05
15 22 0.52
ACGTcount: A:0.52, C:0.00, G:0.24, T:0.24
Consensus pattern (15 bp):
GAAATGATAAGAATT
Found at i:2993321 original size:25 final size:25
Alignment explanation
Indices: 2993290--2993373 Score: 168
Period size: 25 Copynumber: 3.4 Consensus size: 25
2993280 AAGAAGAAAG
2993290 GAAATGATAAGAATTGAAATGGATA
1 GAAATGATAAGAATTGAAATGGATA
2993315 GAAATGATAAGAATTGAAATGGATA
1 GAAATGATAAGAATTGAAATGGATA
2993340 GAAATGATAAGAATTGAAATGGATA
1 GAAATGATAAGAATTGAAATGGATA
2993365 GAAATGATA
1 GAAATGATA
2993374 TCAAAGTGGG
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 59 1.00
ACGTcount: A:0.52, C:0.00, G:0.24, T:0.24
Consensus pattern (25 bp):
GAAATGATAAGAATTGAAATGGATA
Found at i:3004749 original size:9 final size:9
Alignment explanation
Indices: 3004734--3004766 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
3004724 CTCGGGTTAG
3004734 TAAAAAATAA
1 TAAAAAA-AA
3004744 -AAAAAAAA
1 TAAAAAAAA
3004752 TAAAAAAAA
1 TAAAAAAAA
3004761 TAAAAA
1 TAAAAA
3004767 TGTTTAAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 2 0.09
9 20 0.91
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (9 bp):
TAAAAAAAA
Found at i:3004751 original size:11 final size:11
Alignment explanation
Indices: 3004735--3004760 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
3004725 TCGGGTTAGT
3004735 AAAAAATAAAA
1 AAAAAATAAAA
3004746 AAAAAATAAAA
1 AAAAAATAAAA
3004757 AAAA
1 AAAA
3004761 TAAAAATGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (11 bp):
AAAAAATAAAA
Found at i:3009736 original size:8 final size:8
Alignment explanation
Indices: 3009723--3009785 Score: 60
Period size: 8 Copynumber: 8.0 Consensus size: 8
3009713 TTTTTTTTTT
3009723 CAAAAAAA
1 CAAAAAAA
3009731 CAAAAAAA
1 CAAAAAAA
3009739 C-AAAAAA
1 CAAAAAAA
3009746 CAAAAAAA
1 CAAAAAAA
3009754 GGCAAAAAAA
1 --CAAAAAAA
***
3009764 -AAAGGCA
1 CAAAAAAA
3009771 -AAAAAAA
1 CAAAAAAA
3009778 CAAAAAAA
1 CAAAAAAA
3009786 TAGCCAAAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
7 15 0.33
8 22 0.49
10 8 0.18
ACGTcount: A:0.83, C:0.11, G:0.06, T:0.00
Consensus pattern (8 bp):
CAAAAAAA
Found at i:3009753 original size:23 final size:22
Alignment explanation
Indices: 3009723--3009785 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 22
3009713 TTTTTTTTTT
3009723 CAAAAAAACAAAAAAACAAAAAA
1 CAAAAAAACAAAAAAA-AAAAAA
**
3009746 CAAAAAAAGGC-AAAAAAAAAAGG
1 CAAAAAAA--CAAAAAAAAAAAAA
3009769 CAAAAAAAACAAAAAAA
1 C-AAAAAAACAAAAAAA
3009786 TAGCCAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
22 1 0.03
23 19 0.56
24 13 0.38
25 1 0.03
ACGTcount: A:0.83, C:0.11, G:0.06, T:0.00
Consensus pattern (22 bp):
CAAAAAAACAAAAAAAAAAAAA
Found at i:3009762 original size:12 final size:12
Alignment explanation
Indices: 3009747--3009797 Score: 54
Period size: 13 Copynumber: 4.4 Consensus size: 12
3009737 AACAAAAAAC
3009747 AAAAAAAGGCAAA
1 AAAAAAAGGC-AA
3009760 AAAAAAAGGC-A
1 AAAAAAAGGCAA
3009771 AAAAAAA--CAA
1 AAAAAAAGGCAA
* *
3009781 AAAAATAGCCAA
1 AAAAAAAGGCAA
3009793 AAAAA
1 AAAAA
3009798 GCCAAAATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
9 1 0.03
10 7 0.21
11 8 0.24
12 8 0.24
13 10 0.29
ACGTcount: A:0.78, C:0.10, G:0.10, T:0.02
Consensus pattern (12 bp):
AAAAAAAGGCAA
Found at i:3009763 original size:13 final size:13
Alignment explanation
Indices: 3009747--3009777 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
3009737 AACAAAAAAC
3009747 AAAAAAAGGCAAA
1 AAAAAAAGGCAAA
3009760 AAAAAAAGGCAAA
1 AAAAAAAGGCAAA
3009773 AAAAA
1 AAAAA
3009778 CAAAAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.81, C:0.06, G:0.13, T:0.00
Consensus pattern (13 bp):
AAAAAAAGGCAAA
Found at i:3009764 original size:14 final size:14
Alignment explanation
Indices: 3009742--3009777 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
3009732 AAAAAAACAA
3009742 AAAACAAAAAAAGGC
1 AAAA-AAAAAAAGGC
3009757 -AAAAAAAAAAGGC
1 AAAAAAAAAAAGGC
3009770 AAAAAAAA
1 AAAAAAAA
3009778 CAAAAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 10 0.50
14 10 0.50
ACGTcount: A:0.81, C:0.08, G:0.11, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAGGC
Found at i:3009782 original size:20 final size:21
Alignment explanation
Indices: 3009758--3009797 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3009748 AAAAAAGGCA
* *
3009758 AAAAAAAAAGGCAAAAAAAAC
1 AAAAAAATAGCCAAAAAAAAC
3009779 AAAAAAATAGCCAAAAAAA
1 AAAAAAATAGCCAAAAAAA
3009798 GCCAAAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.80, C:0.10, G:0.07, T:0.03
Consensus pattern (21 bp):
AAAAAAATAGCCAAAAAAAAC
Found at i:3009794 original size:10 final size:10
Alignment explanation
Indices: 3009760--3009804 Score: 54
Period size: 10 Copynumber: 4.4 Consensus size: 10
3009750 AAAAGGCAAA
*
3009760 AAAAAAAGGC
1 AAAAAAAGCC
* *
3009770 AAAAAAAACA
1 AAAAAAAGCC
3009780 AAAAAATAGCC
1 AAAAAA-AGCC
3009791 AAAAAAAGCC
1 AAAAAAAGCC
3009801 AAAA
1 AAAA
3009805 TTTCAAAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
10 21 0.72
11 8 0.28
ACGTcount: A:0.76, C:0.13, G:0.09, T:0.02
Consensus pattern (10 bp):
AAAAAAAGCC
Found at i:3018890 original size:11 final size:13
Alignment explanation
Indices: 3018858--3018887 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
3018848 TGGCCAAAGA
3018858 TGAAAAGGTATGT
1 TGAAAAGGTATGT
3018871 TGAAAAGGTATG-
1 TGAAAAGGTATGT
3018883 TGAAA
1 TGAAA
3018888 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:3021870 original size:22 final size:21
Alignment explanation
Indices: 3021844--3021885 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
3021834 GGCTGCGGAA
3021844 ATGATGGTCTTGATGGATGAAG
1 ATGATGGTCTTGAT-GATGAAG
* *
3021866 ATGATGTTGTTGATGATGAA
1 ATGATGGTCTTGATGATGAA
3021886 ATGGAGATGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.29, C:0.02, G:0.33, T:0.36
Consensus pattern (21 bp):
ATGATGGTCTTGATGATGAAG
Found at i:3025925 original size:21 final size:21
Alignment explanation
Indices: 3025886--3025925 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3025876 AAGGAAGATT
*
3025886 AATGAAATGATAAAGATAAGG
1 AATGAAATGATAAAAATAAGG
3025907 AATGAAATGA-AATAAATAA
1 AATGAAATGATAA-AAATAA
3025926 AGGATAGAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.62, C:0.00, G:0.17, T:0.20
Consensus pattern (21 bp):
AATGAAATGATAAAAATAAGG
Found at i:3044719 original size:18 final size:18
Alignment explanation
Indices: 3044679--3044720 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
3044669 TCTCTATCCT
3044679 TTCTT-TATTTCATTTCA
1 TTCTTATATTTCATTTCA
3044696 TTCTTATATTT-ATTTCA
1 TTCTTATATTTCATTTCA
3044713 TTACTTAT
1 TT-CTTAT
3044721 TATTATCCCC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.57
18 10 0.43
ACGTcount: A:0.21, C:0.14, G:0.00, T:0.64
Consensus pattern (18 bp):
TTCTTATATTTCATTTCA
Found at i:3045206 original size:39 final size:41
Alignment explanation
Indices: 3045140--3045232 Score: 156
Period size: 40 Copynumber: 2.3 Consensus size: 41
3045130 GTCACCTCTT
*
3045140 TCTTTTTATACCTTCATTGTCCTTGTCTTC-ACCATTTCTA
1 TCTTTTAATACCTTCATTGTCCTTGTCTTCAACCATTTCTA
3045180 TCTTTTAATACCTTCATTGTCC-TGTCTTCAACCATTTCTA
1 TCTTTTAATACCTTCATTGTCCTTGTCTTCAACCATTTCTA
3045220 TC-TTTAATACCTT
1 TCTTTTAATACCTT
3045233 TAAATCATTT
Statistics
Matches: 51, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
39 18 0.35
40 33 0.65
ACGTcount: A:0.18, C:0.27, G:0.04, T:0.51
Consensus pattern (41 bp):
TCTTTTAATACCTTCATTGTCCTTGTCTTCAACCATTTCTA
Done.